EHV-1 TSS dynamics
Balázs Kakuk
## Error in library(future.apply) :
## there is no package called 'future.apply'Project info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
TSS dynamics
Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.7)... Done.## Bootstrap (r = 0.8)... Done.## Bootstrap (r = 0.9)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.09)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.29)... Done.## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.58)... Done.## Bootstrap (r = 0.69)... Done.## Bootstrap (r = 0.77)... Done.## Bootstrap (r = 0.88)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.08)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.27)... Done.## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Cut the tree at an optimal number of clusters
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 2: 1 ORF4 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 3: 1 ORF5 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 4: 1 ORF7 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 5: 1 ORF9 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 6: 1 ORF10 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 7: 1 ORF17 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 8: 1 ORF20 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 9: 1 ORF21 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 10: 1 ORF30 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 11: 1 ORF31 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 12: 1 ORF34 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 13: 1 ORF38 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 14: 1 ORF50 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 15: 1 ORF53 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 16: 1 ORF56 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 17: 1 ORF61 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 18: 1 ORF63 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 19: 1 NOIR_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 20: 1 ORF65_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 21: 1 ORF67_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 22: 1 ORF69 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 23: 1 NOIR_2 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 24: 2 ORF2 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 25: 2 ORF3 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 26: 2 ORF8 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 27: 2 ORF11 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 28: 2 ORF14 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 29: 2 ORF18 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 30: 2 ORF19 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 31: 2 ORF22 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 32: 2 ORF23 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 33: 2 ORF24 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 34: 2 ORF25 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 35: 2 ORF26 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 36: 2 ORF27 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 37: 2 ORF28 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 38: 2 ORF29 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 39: 2 ORF32 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 40: 2 ORF33 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 41: 2 ORF35.5 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 42: 2 ORF36 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 43: 2 ORF37 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 44: 2 ORF39 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 45: 2 CTO 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 46: 2 ORF40 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 47: 2 ORF42 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 48: 2 ORF43 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 49: 2 ORF44 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 50: 2 ORF46 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 51: 2 ORF49 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 52: 2 ORF51 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 53: 2 ORF55 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 54: 2 ORF58 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 55: 2 ORF59 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 56: 2 ORF62 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 57: 2 ORF66_1 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 58: 2 ORF68 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 59: 2 ORF73 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 60: 2 ORF74 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 61: 2 ORF76 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 62: 3 ORF6 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 63: 3 ORF70 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 64: 4 ORF12 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 65: 4 ORF13 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 66: 4 ORF15 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 67: 4 ORF16 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 68: 4 ORF35 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 69: 4 ORF41 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 70: 4 ORF45 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 71: 4 ORF48 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 72: 4 ORF52 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 73: 4 ORF54 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 74: 4 ORF57 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 75: 4 ORF60 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 76: 4 ORF71 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 77: 4 ORF72 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 78: 5 ORF64_1 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 79: 5 ORF75 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004369945 -1.892748 0.9836849 0.7123394
## 2: 0.004369945 -1.892748 0.9836849 0.7123394
## 3: 0.004369945 -1.892748 0.9836849 0.7123394
## 4: 0.004369945 -1.892748 0.9836849 0.7123394
## 5: 0.004369945 -1.892748 0.9836849 0.7123394
## 6: 0.004369945 -1.892748 0.9836849 0.7123394
## 7: 0.004369945 -1.892748 0.9836849 0.7123394
## 8: 0.004369945 -1.892748 0.9836849 0.7123394
## 9: 0.004369945 -1.892748 0.9836849 0.7123394
## 10: 0.004369945 -1.892748 0.9836849 0.7123394
## 11: 0.004369945 -1.892748 0.9836849 0.7123394
## 12: 0.004369945 -1.892748 0.9836849 0.7123394
## 13: 0.004369945 -1.892748 0.9836849 0.7123394
## 14: 0.004369945 -1.892748 0.9836849 0.7123394
## 15: 0.004369945 -1.892748 0.9836849 0.7123394
## 16: 0.004369945 -1.892748 0.9836849 0.7123394
## 17: 0.004369945 -1.892748 0.9836849 0.7123394
## 18: 0.004369945 -1.892748 0.9836849 0.7123394
## 19: 0.004369945 -1.892748 0.9836849 0.7123394
## 20: 0.004369945 -1.892748 0.9836849 0.7123394
## 21: 0.004369945 -1.892748 0.9836849 0.7123394
## 22: 0.004369945 -1.892748 0.9836849 0.7123394
## 23: 0.004369945 -1.892748 0.9836849 0.7123394
## 24: 0.005047433 -1.075907 0.6315821 0.7673805
## 25: 0.005047433 -1.075907 0.6315821 0.7673805
## 26: 0.005047433 -1.075907 0.6315821 0.7673805
## 27: 0.005047433 -1.075907 0.6315821 0.7673805
## 28: 0.005047433 -1.075907 0.6315821 0.7673805
## 29: 0.005047433 -1.075907 0.6315821 0.7673805
## 30: 0.005047433 -1.075907 0.6315821 0.7673805
## 31: 0.005047433 -1.075907 0.6315821 0.7673805
## 32: 0.005047433 -1.075907 0.6315821 0.7673805
## 33: 0.005047433 -1.075907 0.6315821 0.7673805
## 34: 0.005047433 -1.075907 0.6315821 0.7673805
## 35: 0.005047433 -1.075907 0.6315821 0.7673805
## 36: 0.005047433 -1.075907 0.6315821 0.7673805
## 37: 0.005047433 -1.075907 0.6315821 0.7673805
## 38: 0.005047433 -1.075907 0.6315821 0.7673805
## 39: 0.005047433 -1.075907 0.6315821 0.7673805
## 40: 0.005047433 -1.075907 0.6315821 0.7673805
## 41: 0.005047433 -1.075907 0.6315821 0.7673805
## 42: 0.005047433 -1.075907 0.6315821 0.7673805
## 43: 0.005047433 -1.075907 0.6315821 0.7673805
## 44: 0.005047433 -1.075907 0.6315821 0.7673805
## 45: 0.005047433 -1.075907 0.6315821 0.7673805
## 46: 0.005047433 -1.075907 0.6315821 0.7673805
## 47: 0.005047433 -1.075907 0.6315821 0.7673805
## 48: 0.005047433 -1.075907 0.6315821 0.7673805
## 49: 0.005047433 -1.075907 0.6315821 0.7673805
## 50: 0.005047433 -1.075907 0.6315821 0.7673805
## 51: 0.005047433 -1.075907 0.6315821 0.7673805
## 52: 0.005047433 -1.075907 0.6315821 0.7673805
## 53: 0.005047433 -1.075907 0.6315821 0.7673805
## 54: 0.005047433 -1.075907 0.6315821 0.7673805
## 55: 0.005047433 -1.075907 0.6315821 0.7673805
## 56: 0.005047433 -1.075907 0.6315821 0.7673805
## 57: 0.005047433 -1.075907 0.6315821 0.7673805
## 58: 0.005047433 -1.075907 0.6315821 0.7673805
## 59: 0.005047433 -1.075907 0.6315821 0.7673805
## 60: 0.005047433 -1.075907 0.6315821 0.7673805
## 61: 0.005047433 -1.075907 0.6315821 0.7673805
## 62: 0.004877772 -1.730560 1.0893894 0.9896749
## 63: 0.004877772 -1.730560 1.0893894 0.9896749
## 64: 0.004812618 -1.784042 1.1023833 0.9849542
## 65: 0.004812618 -1.784042 1.1023833 0.9849542
## 66: 0.004812618 -1.784042 1.1023833 0.9849542
## 67: 0.004812618 -1.784042 1.1023833 0.9849542
## 68: 0.004812618 -1.784042 1.1023833 0.9849542
## 69: 0.004812618 -1.784042 1.1023833 0.9849542
## 70: 0.004812618 -1.784042 1.1023833 0.9849542
## 71: 0.004812618 -1.784042 1.1023833 0.9849542
## 72: 0.004812618 -1.784042 1.1023833 0.9849542
## 73: 0.004812618 -1.784042 1.1023833 0.9849542
## 74: 0.004812618 -1.784042 1.1023833 0.9849542
## 75: 0.004812618 -1.784042 1.1023833 0.9849542
## 76: 0.004812618 -1.784042 1.1023833 0.9849542
## 77: 0.004812618 -1.784042 1.1023833 0.9849542
## 78: 0.004577686 -0.504170 1.1633987 0.7284400
## 79: 0.004577686 -0.504170 1.1633987 0.7284400
## se.bp v c pchi
## [1] "ORF67_1" "ORF37" "ORF55" "ORF32" "ORF58" "ORF33" "ORF35.5"
## [8] "ORF25" "ORF27" "ORF62" "ORF45"## [1] 11Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 2: 1 ORF4 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 3: 1 ORF5 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 4: 1 ORF7 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 5: 1 ORF9 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 6: 1 ORF10 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 7: 1 ORF17 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 8: 1 ORF20 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 9: 1 ORF21 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 10: 1 ORF30 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 11: 1 ORF31 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 12: 1 ORF34 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 13: 1 ORF38 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 14: 1 ORF50 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 15: 1 ORF53 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 16: 1 ORF56 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 17: 1 ORF61 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 18: 1 ORF63 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 19: 1 NOIR_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 20: 1 ORF65_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 21: 1 ORF67_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 22: 1 ORF69 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 23: 1 NOIR_2 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 24: 2 ORF2 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 25: 2 ORF3 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 26: 2 ORF11 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 27: 2 ORF14 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 28: 2 ORF18 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 29: 2 ORF19 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 30: 2 ORF26 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 31: 2 ORF28 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 32: 2 ORF29 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 33: 2 ORF37 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 34: 2 ORF51 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 35: 2 ORF55 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 36: 2 ORF66_1 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 37: 2 ORF73 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 38: 2 ORF76 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 39: 3 ORF6 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 40: 3 ORF70 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 41: 4 ORF8 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 42: 4 ORF22 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 43: 4 ORF23 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 44: 4 ORF24 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 45: 4 ORF25 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 46: 4 ORF27 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 47: 4 ORF32 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 48: 4 ORF33 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 49: 4 ORF35.5 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 50: 4 ORF36 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 51: 4 ORF39 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 52: 4 CTO 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 53: 4 ORF40 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 54: 4 ORF42 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 55: 4 ORF43 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 56: 4 ORF44 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 57: 4 ORF46 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 58: 4 ORF49 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 59: 4 ORF58 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 60: 4 ORF59 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 61: 4 ORF62 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 62: 4 ORF68 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 63: 4 ORF74 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 64: 5 ORF12 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 65: 5 ORF13 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 66: 5 ORF15 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 67: 5 ORF16 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 68: 5 ORF35 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 69: 5 ORF41 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 70: 5 ORF45 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 71: 5 ORF48 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 72: 5 ORF52 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 73: 5 ORF54 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 74: 5 ORF57 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 75: 5 ORF60 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 76: 5 ORF71 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 77: 5 ORF72 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 78: 6 ORF64_1 0.9021746 0.9817929 0.6208402 0.013898375 0.0035533319
## 79: 6 ORF75 0.9021746 0.9817929 0.6208402 0.013898375 0.0035533319
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004369945 -1.892748 0.9836849 0.7123394
## 2: 0.004369945 -1.892748 0.9836849 0.7123394
## 3: 0.004369945 -1.892748 0.9836849 0.7123394
## 4: 0.004369945 -1.892748 0.9836849 0.7123394
## 5: 0.004369945 -1.892748 0.9836849 0.7123394
## 6: 0.004369945 -1.892748 0.9836849 0.7123394
## 7: 0.004369945 -1.892748 0.9836849 0.7123394
## 8: 0.004369945 -1.892748 0.9836849 0.7123394
## 9: 0.004369945 -1.892748 0.9836849 0.7123394
## 10: 0.004369945 -1.892748 0.9836849 0.7123394
## 11: 0.004369945 -1.892748 0.9836849 0.7123394
## 12: 0.004369945 -1.892748 0.9836849 0.7123394
## 13: 0.004369945 -1.892748 0.9836849 0.7123394
## 14: 0.004369945 -1.892748 0.9836849 0.7123394
## 15: 0.004369945 -1.892748 0.9836849 0.7123394
## 16: 0.004369945 -1.892748 0.9836849 0.7123394
## 17: 0.004369945 -1.892748 0.9836849 0.7123394
## 18: 0.004369945 -1.892748 0.9836849 0.7123394
## 19: 0.004369945 -1.892748 0.9836849 0.7123394
## 20: 0.004369945 -1.892748 0.9836849 0.7123394
## 21: 0.004369945 -1.892748 0.9836849 0.7123394
## 22: 0.004369945 -1.892748 0.9836849 0.7123394
## 23: 0.004369945 -1.892748 0.9836849 0.7123394
## 24: 0.005047433 -1.075907 0.6315821 0.7673805
## 25: 0.005047433 -1.075907 0.6315821 0.7673805
## 26: 0.005047433 -1.075907 0.6315821 0.7673805
## 27: 0.005047433 -1.075907 0.6315821 0.7673805
## 28: 0.005047433 -1.075907 0.6315821 0.7673805
## 29: 0.005047433 -1.075907 0.6315821 0.7673805
## 30: 0.005047433 -1.075907 0.6315821 0.7673805
## 31: 0.005047433 -1.075907 0.6315821 0.7673805
## 32: 0.005047433 -1.075907 0.6315821 0.7673805
## 33: 0.005047433 -1.075907 0.6315821 0.7673805
## 34: 0.005047433 -1.075907 0.6315821 0.7673805
## 35: 0.005047433 -1.075907 0.6315821 0.7673805
## 36: 0.005047433 -1.075907 0.6315821 0.7673805
## 37: 0.005047433 -1.075907 0.6315821 0.7673805
## 38: 0.005047433 -1.075907 0.6315821 0.7673805
## 39: 0.004877772 -1.730560 1.0893894 0.9896749
## 40: 0.004877772 -1.730560 1.0893894 0.9896749
## 41: 0.004812618 -1.784042 1.1023833 0.9849542
## 42: 0.004812618 -1.784042 1.1023833 0.9849542
## 43: 0.004812618 -1.784042 1.1023833 0.9849542
## 44: 0.004812618 -1.784042 1.1023833 0.9849542
## 45: 0.004812618 -1.784042 1.1023833 0.9849542
## 46: 0.004812618 -1.784042 1.1023833 0.9849542
## 47: 0.004812618 -1.784042 1.1023833 0.9849542
## 48: 0.004812618 -1.784042 1.1023833 0.9849542
## 49: 0.004812618 -1.784042 1.1023833 0.9849542
## 50: 0.004812618 -1.784042 1.1023833 0.9849542
## 51: 0.004812618 -1.784042 1.1023833 0.9849542
## 52: 0.004812618 -1.784042 1.1023833 0.9849542
## 53: 0.004812618 -1.784042 1.1023833 0.9849542
## 54: 0.004812618 -1.784042 1.1023833 0.9849542
## 55: 0.004812618 -1.784042 1.1023833 0.9849542
## 56: 0.004812618 -1.784042 1.1023833 0.9849542
## 57: 0.004812618 -1.784042 1.1023833 0.9849542
## 58: 0.004812618 -1.784042 1.1023833 0.9849542
## 59: 0.004812618 -1.784042 1.1023833 0.9849542
## 60: 0.004812618 -1.784042 1.1023833 0.9849542
## 61: 0.004812618 -1.784042 1.1023833 0.9849542
## 62: 0.004812618 -1.784042 1.1023833 0.9849542
## 63: 0.004812618 -1.784042 1.1023833 0.9849542
## 64: 0.004577686 -0.504170 1.1633987 0.7284400
## 65: 0.004577686 -0.504170 1.1633987 0.7284400
## 66: 0.004577686 -0.504170 1.1633987 0.7284400
## 67: 0.004577686 -0.504170 1.1633987 0.7284400
## 68: 0.004577686 -0.504170 1.1633987 0.7284400
## 69: 0.004577686 -0.504170 1.1633987 0.7284400
## 70: 0.004577686 -0.504170 1.1633987 0.7284400
## 71: 0.004577686 -0.504170 1.1633987 0.7284400
## 72: 0.004577686 -0.504170 1.1633987 0.7284400
## 73: 0.004577686 -0.504170 1.1633987 0.7284400
## 74: 0.004577686 -0.504170 1.1633987 0.7284400
## 75: 0.004577686 -0.504170 1.1633987 0.7284400
## 76: 0.004577686 -0.504170 1.1633987 0.7284400
## 77: 0.004577686 -0.504170 1.1633987 0.7284400
## 78: 0.005235101 -1.199980 0.8922918 0.2195588
## 79: 0.005235101 -1.199980 0.8922918 0.2195588
## se.bp v c pchi
## [1] "ORF38" "ORF67_1" "ORF9" "ORF11" "ORF14" "ORF2" "ORF73"
## [8] "ORF49" "ORF27" "ORF32" "ORF62" "ORF45"## [1] 12Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 2: 1 ORF4 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 3: 1 ORF5 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 4: 1 ORF7 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 5: 1 ORF9 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 6: 1 ORF10 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 7: 1 ORF17 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 8: 1 ORF20 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 9: 1 ORF21 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 10: 1 ORF30 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 11: 1 ORF31 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 12: 1 ORF34 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 13: 1 ORF38 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 14: 1 ORF50 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 15: 1 ORF53 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 16: 1 ORF56 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 17: 1 ORF61 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 18: 1 ORF63 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 19: 1 NOIR_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 20: 1 ORF65_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 21: 1 ORF67_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 22: 1 ORF69 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 23: 1 NOIR_2 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 24: 2 ORF2 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 25: 2 ORF3 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 26: 2 ORF11 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 27: 2 ORF14 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 28: 2 ORF18 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 29: 2 ORF19 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 30: 2 ORF26 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 31: 2 ORF28 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 32: 2 ORF29 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 33: 2 ORF37 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 34: 2 ORF51 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 35: 2 ORF55 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 36: 2 ORF66_1 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 37: 2 ORF73 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 38: 2 ORF76 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 39: 3 ORF6 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 40: 3 ORF70 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 41: 4 ORF8 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 42: 4 ORF22 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 43: 4 ORF23 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 44: 4 ORF24 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 45: 4 ORF25 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 46: 4 ORF27 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 47: 4 ORF32 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 48: 4 ORF33 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 49: 4 ORF35.5 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 50: 4 ORF36 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 51: 4 ORF39 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 52: 4 CTO 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 53: 4 ORF40 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 54: 4 ORF42 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 55: 4 ORF43 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 56: 4 ORF44 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 57: 4 ORF46 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 58: 4 ORF49 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 59: 4 ORF58 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 60: 4 ORF59 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 61: 4 ORF62 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 62: 4 ORF68 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 63: 4 ORF74 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 64: 5 ORF12 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 65: 5 ORF13 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 66: 5 ORF15 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 67: 5 ORF16 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 68: 5 ORF35 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 69: 5 ORF41 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 70: 5 ORF48 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 71: 5 ORF52 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 72: 5 ORF54 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 73: 5 ORF57 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 74: 5 ORF60 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 75: 5 ORF71 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 76: 5 ORF72 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 77: 6 ORF45 0.9021746 0.9817929 0.6208402 0.013898375 0.0035533319
## 78: 7 ORF64_1 0.9495836 0.9906825 0.7117112 0.008344940 0.0020460314
## 79: 7 ORF75 0.9495836 0.9906825 0.7117112 0.008344940 0.0020460314
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004369945 -1.892748 0.9836849 0.7123394
## 2: 0.004369945 -1.892748 0.9836849 0.7123394
## 3: 0.004369945 -1.892748 0.9836849 0.7123394
## 4: 0.004369945 -1.892748 0.9836849 0.7123394
## 5: 0.004369945 -1.892748 0.9836849 0.7123394
## 6: 0.004369945 -1.892748 0.9836849 0.7123394
## 7: 0.004369945 -1.892748 0.9836849 0.7123394
## 8: 0.004369945 -1.892748 0.9836849 0.7123394
## 9: 0.004369945 -1.892748 0.9836849 0.7123394
## 10: 0.004369945 -1.892748 0.9836849 0.7123394
## 11: 0.004369945 -1.892748 0.9836849 0.7123394
## 12: 0.004369945 -1.892748 0.9836849 0.7123394
## 13: 0.004369945 -1.892748 0.9836849 0.7123394
## 14: 0.004369945 -1.892748 0.9836849 0.7123394
## 15: 0.004369945 -1.892748 0.9836849 0.7123394
## 16: 0.004369945 -1.892748 0.9836849 0.7123394
## 17: 0.004369945 -1.892748 0.9836849 0.7123394
## 18: 0.004369945 -1.892748 0.9836849 0.7123394
## 19: 0.004369945 -1.892748 0.9836849 0.7123394
## 20: 0.004369945 -1.892748 0.9836849 0.7123394
## 21: 0.004369945 -1.892748 0.9836849 0.7123394
## 22: 0.004369945 -1.892748 0.9836849 0.7123394
## 23: 0.004369945 -1.892748 0.9836849 0.7123394
## 24: 0.005047433 -1.075907 0.6315821 0.7673805
## 25: 0.005047433 -1.075907 0.6315821 0.7673805
## 26: 0.005047433 -1.075907 0.6315821 0.7673805
## 27: 0.005047433 -1.075907 0.6315821 0.7673805
## 28: 0.005047433 -1.075907 0.6315821 0.7673805
## 29: 0.005047433 -1.075907 0.6315821 0.7673805
## 30: 0.005047433 -1.075907 0.6315821 0.7673805
## 31: 0.005047433 -1.075907 0.6315821 0.7673805
## 32: 0.005047433 -1.075907 0.6315821 0.7673805
## 33: 0.005047433 -1.075907 0.6315821 0.7673805
## 34: 0.005047433 -1.075907 0.6315821 0.7673805
## 35: 0.005047433 -1.075907 0.6315821 0.7673805
## 36: 0.005047433 -1.075907 0.6315821 0.7673805
## 37: 0.005047433 -1.075907 0.6315821 0.7673805
## 38: 0.005047433 -1.075907 0.6315821 0.7673805
## 39: 0.004877772 -1.730560 1.0893894 0.9896749
## 40: 0.004877772 -1.730560 1.0893894 0.9896749
## 41: 0.004812618 -1.784042 1.1023833 0.9849542
## 42: 0.004812618 -1.784042 1.1023833 0.9849542
## 43: 0.004812618 -1.784042 1.1023833 0.9849542
## 44: 0.004812618 -1.784042 1.1023833 0.9849542
## 45: 0.004812618 -1.784042 1.1023833 0.9849542
## 46: 0.004812618 -1.784042 1.1023833 0.9849542
## 47: 0.004812618 -1.784042 1.1023833 0.9849542
## 48: 0.004812618 -1.784042 1.1023833 0.9849542
## 49: 0.004812618 -1.784042 1.1023833 0.9849542
## 50: 0.004812618 -1.784042 1.1023833 0.9849542
## 51: 0.004812618 -1.784042 1.1023833 0.9849542
## 52: 0.004812618 -1.784042 1.1023833 0.9849542
## 53: 0.004812618 -1.784042 1.1023833 0.9849542
## 54: 0.004812618 -1.784042 1.1023833 0.9849542
## 55: 0.004812618 -1.784042 1.1023833 0.9849542
## 56: 0.004812618 -1.784042 1.1023833 0.9849542
## 57: 0.004812618 -1.784042 1.1023833 0.9849542
## 58: 0.004812618 -1.784042 1.1023833 0.9849542
## 59: 0.004812618 -1.784042 1.1023833 0.9849542
## 60: 0.004812618 -1.784042 1.1023833 0.9849542
## 61: 0.004812618 -1.784042 1.1023833 0.9849542
## 62: 0.004812618 -1.784042 1.1023833 0.9849542
## 63: 0.004812618 -1.784042 1.1023833 0.9849542
## 64: 0.004577686 -0.504170 1.1633987 0.7284400
## 65: 0.004577686 -0.504170 1.1633987 0.7284400
## 66: 0.004577686 -0.504170 1.1633987 0.7284400
## 67: 0.004577686 -0.504170 1.1633987 0.7284400
## 68: 0.004577686 -0.504170 1.1633987 0.7284400
## 69: 0.004577686 -0.504170 1.1633987 0.7284400
## 70: 0.004577686 -0.504170 1.1633987 0.7284400
## 71: 0.004577686 -0.504170 1.1633987 0.7284400
## 72: 0.004577686 -0.504170 1.1633987 0.7284400
## 73: 0.004577686 -0.504170 1.1633987 0.7284400
## 74: 0.004577686 -0.504170 1.1633987 0.7284400
## 75: 0.004577686 -0.504170 1.1633987 0.7284400
## 76: 0.004577686 -0.504170 1.1633987 0.7284400
## 77: 0.005235101 -1.199980 0.8922918 0.2195588
## 78: 0.004959583 -1.455571 0.8971807 0.7216489
## 79: 0.004959583 -1.455571 0.8971807 0.7216489
## se.bp v c pchi
## [1] "ORF38" "ORF67_1" "ORF9" "ORF11" "ORF14" "ORF2" "ORF73"
## [8] "ORF25" "ORF49" "ORF27" "ORF32" "ORF62" "ORF45"## [1] 13Selected number of clusters: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 2: 1 ORF4 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 3: 1 ORF5 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 4: 1 ORF7 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 5: 1 ORF9 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 6: 1 ORF10 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 7: 1 ORF17 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 8: 1 ORF20 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 9: 1 ORF21 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 10: 1 ORF30 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 11: 1 ORF31 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 12: 1 ORF34 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 13: 1 ORF38 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 14: 1 ORF50 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 15: 1 ORF53 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 16: 1 ORF56 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 17: 1 ORF61 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 18: 1 ORF63 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 19: 1 NOIR_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 20: 1 ORF65_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 21: 1 ORF67_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 22: 1 ORF69 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 23: 1 NOIR_2 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 24: 2 ORF2 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 25: 2 ORF3 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 26: 2 ORF11 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 27: 2 ORF14 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 28: 2 ORF18 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 29: 2 ORF19 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 30: 2 ORF26 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 31: 2 ORF28 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 32: 2 ORF29 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 33: 2 ORF37 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 34: 2 ORF51 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 35: 2 ORF55 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 36: 2 ORF66_1 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 37: 2 ORF73 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 38: 2 ORF76 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 39: 3 ORF6 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 40: 3 ORF70 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 41: 4 ORF8 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 42: 4 ORF22 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 43: 4 ORF23 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 44: 4 ORF24 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 45: 4 ORF25 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 46: 4 ORF27 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 47: 4 ORF32 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 48: 4 ORF33 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 49: 4 ORF35.5 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 50: 4 ORF36 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 51: 4 ORF39 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 52: 4 CTO 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 53: 4 ORF40 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 54: 4 ORF42 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 55: 4 ORF43 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 56: 4 ORF44 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 57: 4 ORF46 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 58: 4 ORF49 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 59: 4 ORF58 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 60: 4 ORF59 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 61: 4 ORF62 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 62: 4 ORF68 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 63: 4 ORF74 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 64: 5 ORF12 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 65: 5 ORF13 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 66: 5 ORF15 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 67: 5 ORF16 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 68: 5 ORF35 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 69: 5 ORF41 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 70: 5 ORF48 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 71: 5 ORF52 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 72: 5 ORF54 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 73: 5 ORF57 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 74: 5 ORF60 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 75: 5 ORF71 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 76: 5 ORF72 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 77: 6 ORF45 0.9021746 0.9817929 0.6208402 0.013898375 0.0035533319
## 78: 7 ORF64_1 0.9495836 0.9906825 0.7117112 0.008344940 0.0020460314
## 79: 7 ORF75 0.9495836 0.9906825 0.7117112 0.008344940 0.0020460314
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004369945 -1.892748 0.9836849 0.7123394
## 2: 0.004369945 -1.892748 0.9836849 0.7123394
## 3: 0.004369945 -1.892748 0.9836849 0.7123394
## 4: 0.004369945 -1.892748 0.9836849 0.7123394
## 5: 0.004369945 -1.892748 0.9836849 0.7123394
## 6: 0.004369945 -1.892748 0.9836849 0.7123394
## 7: 0.004369945 -1.892748 0.9836849 0.7123394
## 8: 0.004369945 -1.892748 0.9836849 0.7123394
## 9: 0.004369945 -1.892748 0.9836849 0.7123394
## 10: 0.004369945 -1.892748 0.9836849 0.7123394
## 11: 0.004369945 -1.892748 0.9836849 0.7123394
## 12: 0.004369945 -1.892748 0.9836849 0.7123394
## 13: 0.004369945 -1.892748 0.9836849 0.7123394
## 14: 0.004369945 -1.892748 0.9836849 0.7123394
## 15: 0.004369945 -1.892748 0.9836849 0.7123394
## 16: 0.004369945 -1.892748 0.9836849 0.7123394
## 17: 0.004369945 -1.892748 0.9836849 0.7123394
## 18: 0.004369945 -1.892748 0.9836849 0.7123394
## 19: 0.004369945 -1.892748 0.9836849 0.7123394
## 20: 0.004369945 -1.892748 0.9836849 0.7123394
## 21: 0.004369945 -1.892748 0.9836849 0.7123394
## 22: 0.004369945 -1.892748 0.9836849 0.7123394
## 23: 0.004369945 -1.892748 0.9836849 0.7123394
## 24: 0.005047433 -1.075907 0.6315821 0.7673805
## 25: 0.005047433 -1.075907 0.6315821 0.7673805
## 26: 0.005047433 -1.075907 0.6315821 0.7673805
## 27: 0.005047433 -1.075907 0.6315821 0.7673805
## 28: 0.005047433 -1.075907 0.6315821 0.7673805
## 29: 0.005047433 -1.075907 0.6315821 0.7673805
## 30: 0.005047433 -1.075907 0.6315821 0.7673805
## 31: 0.005047433 -1.075907 0.6315821 0.7673805
## 32: 0.005047433 -1.075907 0.6315821 0.7673805
## 33: 0.005047433 -1.075907 0.6315821 0.7673805
## 34: 0.005047433 -1.075907 0.6315821 0.7673805
## 35: 0.005047433 -1.075907 0.6315821 0.7673805
## 36: 0.005047433 -1.075907 0.6315821 0.7673805
## 37: 0.005047433 -1.075907 0.6315821 0.7673805
## 38: 0.005047433 -1.075907 0.6315821 0.7673805
## 39: 0.004877772 -1.730560 1.0893894 0.9896749
## 40: 0.004877772 -1.730560 1.0893894 0.9896749
## 41: 0.004812618 -1.784042 1.1023833 0.9849542
## 42: 0.004812618 -1.784042 1.1023833 0.9849542
## 43: 0.004812618 -1.784042 1.1023833 0.9849542
## 44: 0.004812618 -1.784042 1.1023833 0.9849542
## 45: 0.004812618 -1.784042 1.1023833 0.9849542
## 46: 0.004812618 -1.784042 1.1023833 0.9849542
## 47: 0.004812618 -1.784042 1.1023833 0.9849542
## 48: 0.004812618 -1.784042 1.1023833 0.9849542
## 49: 0.004812618 -1.784042 1.1023833 0.9849542
## 50: 0.004812618 -1.784042 1.1023833 0.9849542
## 51: 0.004812618 -1.784042 1.1023833 0.9849542
## 52: 0.004812618 -1.784042 1.1023833 0.9849542
## 53: 0.004812618 -1.784042 1.1023833 0.9849542
## 54: 0.004812618 -1.784042 1.1023833 0.9849542
## 55: 0.004812618 -1.784042 1.1023833 0.9849542
## 56: 0.004812618 -1.784042 1.1023833 0.9849542
## 57: 0.004812618 -1.784042 1.1023833 0.9849542
## 58: 0.004812618 -1.784042 1.1023833 0.9849542
## 59: 0.004812618 -1.784042 1.1023833 0.9849542
## 60: 0.004812618 -1.784042 1.1023833 0.9849542
## 61: 0.004812618 -1.784042 1.1023833 0.9849542
## 62: 0.004812618 -1.784042 1.1023833 0.9849542
## 63: 0.004812618 -1.784042 1.1023833 0.9849542
## 64: 0.004577686 -0.504170 1.1633987 0.7284400
## 65: 0.004577686 -0.504170 1.1633987 0.7284400
## 66: 0.004577686 -0.504170 1.1633987 0.7284400
## 67: 0.004577686 -0.504170 1.1633987 0.7284400
## 68: 0.004577686 -0.504170 1.1633987 0.7284400
## 69: 0.004577686 -0.504170 1.1633987 0.7284400
## 70: 0.004577686 -0.504170 1.1633987 0.7284400
## 71: 0.004577686 -0.504170 1.1633987 0.7284400
## 72: 0.004577686 -0.504170 1.1633987 0.7284400
## 73: 0.004577686 -0.504170 1.1633987 0.7284400
## 74: 0.004577686 -0.504170 1.1633987 0.7284400
## 75: 0.004577686 -0.504170 1.1633987 0.7284400
## 76: 0.004577686 -0.504170 1.1633987 0.7284400
## 77: 0.005235101 -1.199980 0.8922918 0.2195588
## 78: 0.004959583 -1.455571 0.8971807 0.7216489
## 79: 0.004959583 -1.455571 0.8971807 0.7216489
## se.bp v c pchi
## [1] "ORF38" "ORF67_1" "ORF9" "ORF11" "ORF14" "ORF2" "ORF73"
## [8] "ORF25" "ORF49" "ORF27" "ORF32" "ORF62" "ORF45"## [1] 13Remove genes from clusters ?
## The following genes were removed from their corresponding clusters
## as their silhouette widths were lower than 0.1 and their distance from the group centroid was higher than 0.5:
## ORF38
## ORF67_1
## ORF9
## ORF11
## ORF14
## ORF2
## ORF73
## ORF25
## ORF49
## ORF27
## ORF32
## ORF62
## ORF45Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
